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BigNASim
Entry: NAFlex_implSolvMD_CG
Nucleic Acid Data:
Sequence
GCAACGTGCTATGGAAGC
Rev. Sequence
GCTTCCATAGCACGTTGC
Type
DNA
SubType
B
Chains
duplex
Pdb
-
Ligands
No
Keywords
DNA-B Duplex Naked
MD Simulation >>
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Simulation Metadata
Force Field
parmBSC1
Simulation Date
0.00000000 1720483200
Simulated Time
1,000
Time Step
20 ps
Parts
DNA
Temperature
298K
Water
No
Additional Solvent
No
Counter Ions
No
Ionic Concentration
No
Additional Ions
No
Additional Molecules
No
Ions Parameters
No
Unified Molecular Modeling (UMM) Metadata
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full
UMM)
Simulation Metadata (UMM)
AdditionalIons
No
AdditionalMolecules
No
AdditionalSolvent
No
Author
D.F.
Chains
duplex
Comments
CGeNArate: A Sequence-Dependent Coarse-Grained Model of DNA for Accurate Atomistic MD Simulations of kb-long Duplexes, DOI: 10.1093/nar/gkae444
CounterIons
No
Format
netcdf
FrameStep
20 ps
Frames
50000
IonicConcentration
No
IonsParameters
No
Ligands
No
NucType
DNA
PDB
NONE
Parts
DNA
RMSd_avg
3.697
RMSd_stdev
0.900
Rgyr_avg
18.519
Rgyr_stdev
0.885
SASA_avg
6203.937
SASA_stdev
186.446
SubType
B
Temperature
298K
Topology
AtomACGT.pdb
Trajectory
AtomACGTAll_reduced.nc
Water
No
_id
NAFlex_implSolvMD_CG
dataset
Array
date
0.00000000 1720483200
description
DNA-B Duplex Naked
forceField
CGeNArate
ionsModel
-
moleculeType
Dna
rev_sequence
GCTTCCATAGCACGTTGC
saltConcentration
-
sequence
GCAACGTGCTATGGAAGC
soluteAtoms
1140
soluteCharge
-34
soluteResidues
36
solventAtoms
-
solventResidues
-
time
1,000
totalAtoms
1140
totalCharge
-34
totalIons
-
totalResidues
36
Quality Control
RMSd
-
Rgyr
-
SASA
-
RMSf
-
Trajectory Analyses >>
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